Frequently Asked Questions

General

Where is my data stored? Is it safe? Can I get it out again?

Your library (reference data, notes, folders, labels) is
stored safely in our database. The data is stored
redundantly on multiple servers and we keep continuous
backups in a completely different data center. You can
export your library in common file formats (RIS and BibTeX)
for use with other software. In addition, you can
download all your data in machine readable JSON
format.

Your PDF files and all other files in your library are
stored on Google Drive, Google's cloud storage
service. Using the Google Drive client for Mac and Windows
you can keep a backup of all your files on your local hard
disk.

Where can I run Paperpile? Does it run on Firefox/Safari?

Paperpile is fully supported on Chrome for Mac OS X,
Windows, Linux and Chrome OS. It also
known to run on the open-source Chromium browser. Since
Paperpile uses advanced features of the Chrome platform, it is
not available on other browsers.

I'm missing feature X, will you add it?

Please be patient, Paperpile has just started and we will
add features continuously. Some of the most frequently
requested features that are on our roadmap: Shared folders (added 1/2014, see blog post),
full-text PDF search, PDF annotations, Word plugin.

I'm having problems running Paperpile or found a bug, what
do I do?

If you experience problems first read
our guides and
our troubleshooting page,
which cover the most common issues. Also try to reload the
Paperpile tab and/or restart Chrome; this can help solve some
temporary problems.

Using Paperpile

Can I filter my papers by multiple criteria?

Yes. Use the Shift key when clicking on a folder or label to add additional filters.

How does Paperpile search my library? Can I choose a
specific field to search?

Paperpile searches within most textual data fields from
your papers including title, abstract, author names, journal,
publication year, notes, and identifiers (DOI, PMID,
etc.). Searching within a specific field is not currently
supported, but you can filter your library by a specific
author, year or journal name by clicking on the author /
journal / year from an item in your library.

File syncing

Where are my files stored?

If you import a file to Paperpile a local copy will be
stored within Chrome. This allows you to quickly view your
files without re-downloading them every time. If you enable
syncing to Google Drive, your files will be stored in the
folder 'Paperpile' in your Google Drive space. Once synced,
your files can be accessed when you run Paperpile on different
computers or for reading on a mobile device.

Can I change how files are organized in Google Drive?

Files are organized in subfolders sorted alphabetically by
the first author's last name. At the moment it is not possible
to customize this structure (many users wish to use the same
folders / labels created in Paperpile). This limitation is
mainly for technical reasons, and we hope to offer this highly
requested feature in the future.

Tip: Starred papers are organized in a special
folder, which is useful for example to create a reading list
for quick access on your mobile device.

I already have my PDFs in Google Drive, can I import them directly from there?

No. For privacy reasons Paperpile can only access files that
were uploaded by Paperpile and are stored in the Paperpile
folder. So Paperpile can't access your PDFs that you already
have in some other location in your Google Drive. We suggest
to sync the files to your local hard drive and upload them
again from there.

What can I do if my files are not synced correctly?

In most cases your files will be synced completely
automatically and there is no manual action required. If you
run into problems, check out our file syncing guide.

Google Docs integration

These are a few commonly asked
questions about the Google Docs integration. To learn how to
use the Google Docs plug-in, view our guide on Writing papers in Google Docs.

How does it work? Where are my citations stored?

When you cite an article in a Google Doc, the citation
data is copied from your personal library to a separate
library created just for that document. When you choose a
citation style and click Paperpile > Format
citations Paperpile will format the citations, create a
bibliography, and re-insert the formatted text into your
document.

You can seamlessly collaborate with other Paperpile users
on a single document, adding citations and seeing each others'
changes in real time. And because all references are stored in
a central library, there's no need to worry about keeping
everyone's personal libraries in sync — it just works.

If you work with collaborators who aren't yet using
Paperpile, they can still help edit the manuscript and view a
document's citations: each citation and bibliography item
links to a page where you can view / edit the citation.

What happens if I cite something and then my collaborator
tries to format the document? Will it still work?

Yes! Any author with Paperpile can format the entire
manuscript without any trouble. Since every citation is added
to the same document library, all of the data required to
format a document is stored with the document rather
than in each user's personal library.

Paperpile does not have a citation style for my journal. What can I do?

Paperpile uses the Citation Style Language (CSL) to format
citations and supports thousands of different journal styles
maintained
at citationstyles.org. If
there is no style for a particular journal, chances are that
there are identical or very similar styles you can use. To
find the right style you can use "search by example" tool:
http://editor.citationstyles.org/searchByExample

Plans and pricing

How does the subscription work?

It's easy. Pick a plan and pay securely with any major credit
card. Your trial account will be upgraded immediately.

Your
credit card is charged annually as long as your subscription is
active. You can cancel at any time, and we won't charge your
credit card again.

How do I buy a group license?

Choose a plan and enter 2 or more users in the subscription
form. We will send you a license key valid for the desired number
of accounts — share this key with your colleagues to
activate their accounts. If you need to add more users, you can
view or change the number of users at any time using the license
dashboard.

What about site licenses?

Can I pay with PayPal or via invoice?

Yes. Contact support@paperpile.com with
the plan you want to subscribe to. We will send you a license key
and an invoice you can pay with PayPal or any other way you
prefer.

Tutorials & Guides

Getting started

First thing's first —
you'll want to add some papers to your new library to learn
how to organize your papers and work effectively with
Paperpile. Read on for some tips on how to quickly make the
most out of Paperpile.

Click the Paperpile button in your browser toolbar to import from hundreds of supported publishers' sites. A green arrow appears on the button when you're viewing a supported site (For an example visit doi.org/10.1038/nature10530).

Get organized

Next, add some folders and labels to help keep things
tidy. Click the New Folder button to add a new folder. You
can rearrange your folders by dragging (labels are sorted
automatically).

Drag a paper into a folder using the drag handle on
the left side of the paper, or use the toolbar buttons
to organize many papers at once.

Cite, copy, paste

You can quickly copy and paste formatted citations using
the copy button . Choose
between copying the plain citation string, a rich-text version
with abstract & links (good for emailing), or the Bibtex data
for manuscript preparation.

What's next

But more importantly, Paperpile makes reference management
easy so your next step can be to get back to doing
what you do best — research!

Import your library & PDFs

Ready to make the switch? Easily
import your existing reference library from most popular
software directly into Paperpile — here you'll find
complete instructions for migrating from Mendeley, Zotero, Papers, EndNote, Citavi, or other
software. Or, just add your
PDFs directly and let Paperpile organize them for you!

Mendeley

If your library is fully synced online: If you keep all
your articles and PDFs synced in Mendeley, Paperpile can
automatically import your Mendeley library and PDFs from the
web with one click. Open the "Add Papers" menu, choose
and then follow the on-screen options.

If your library is not synced: Your
Mendeley library and PDFs can still be imported with a few
easy steps:

Find the folder where your Mendeley PDFs are stored
by right-clicking on an item with a PDF and choosing
Open Folder. Navigate to the folder that holds
all of your Mendeley PDFs, and keep that folder open for the
next step.

In Paperpile open the "Add Papers" menu, choose
and add both your exported RIS file and your entire Mendeley
PDF folder to the upload dialog. Click Start
upload to begin.

Paperpile will import your library and attach all
existing PDFs to their correct articles when possible. When
the import is complete, double-check any articles marked as
incomplete or duplicates to help keep your
library clean.

Zotero

If your Zotero library is synced online: Paperpile can
automatically import your Zotero library and attachments from the
web with one click. Open the "Add Papers" menu, choose
and then follow the on-screen options. Note: Private group libraries will not be imported when
"Accept Defaults" is selected. In order to import also private group libraries click
"Change Permissions" and select in "Default Group Permissions" the "Read Only" option.

If your library is not synced: Import your
Zotero library and PDFs with a few simple steps:

In Paperpile open the "Add Papers" menu, choose
and add your exported Zotero folder to the upload dialog. Click Start
upload to begin.

Paperpile will import your Zotero library and attach
each PDF or attachment to its correct article where
possible. When import is complete, double-check any articles
marked as incomplete or duplicates to help
keep your library clean.

Papers

Import your Papers library and PDFs into Paperpile with
just a few clicks:

Now locate your Papers Library directory. Go to File > Preferences
in the Papers menu. The location of your library will be listed in the Library tab
of the Preferences window. Go to the library folder and find the Files
folder within it. Keep this Files folder open for the next step.

In Paperpile open the "Add Papers" menu, choose
and add both your exported RIS file and your entire
Files folder to the upload dialog. Click
Start upload to begin.

Paperpile will import your library and attach all
existing PDFs to their correct articles when possible. When
the import is complete, double-check any articles marked as
incomplete or duplicates to help keep your
library clean.

EndNote

Any EndNote library, including attached PDFs, can be easily
imported into Paperpile with just a few steps.

First, open your EndNote library and export it to
your computer in RefMan (RIS) format: click File > Export..., choose Save as
type "XML", and under output style
choose "Select Another Style" (example). This will open up a new
dialog; choose EndNote Export. Make
sure to uncheck "export selected references" to ensure that
your entire library is exported (example). Click Save to save this file to your
desktop.

Second, find the ".Data" folder that holds your
library's PDFs. For most libraries, EndNote creates a folder
in the same directory as your EndNote library file. It has
the same name as your library with the suffix ".Data"
appended (example). Keep this folder open for
the next step.

Back in Paperpile, open the "Add Papers" menu, choose
and add both your exported RIS file and
the entire ".Data" folder to the upload dialog. You can add them either
by dragging them onto the drop area, or by using the "Choose file(s)/Choose a folder" buttons.
Once you see your RIS and folder in the list of selected filed, click
Start upload to begin.

Paperpile will import your EndNote library and attach
all existing PDFs to their correct articles when
possible. When the import is complete, double-check any
articles marked as incomplete or duplicates to
help keep your library clean.

Citavi

Citavi 5 and Citavi 6 libraries can be easily
imported into Paperpile with just a few steps.

First, open Citavi and create a backup of your project.
You will find this option in the File menu.

Second, locate the backup on your computer. It's a file
with the file ending with ctv5bak or
ctv6bak. The backup file is actually a
zip file. In order to extract it,
replace the Citavi file ending with zip.

Once, the zip file is extracted, you should see
ctv5 or ctv6 files. These
files can directly be uploaded to Paperpile.

Back in Paperpile, open the "Add Papers" menu, choose
and add the extracted ctv5 or ctv6 files to the upload dialog. Click Start upload to begin.

Other reference
managers

If your reference manager supports exporting to either
Bibtex or RIS format, you can simply export your library to a
file and import to Paperpile using the
function.

If you cannot export your library to a standard file
format, Paperpile may be able to extract metadata from your
PDFs themselves — see below.

Unorganized PDFs

In many cases, useful reference metadata can be extracted
even from a collection of unorganized PDFs. Simply drag and
drop some files into the window (example) and
click Start upload to begin.

Paperpile will parse each PDF and use all detectable
metadata (including data fetched online from databases like
PubMed) to import the article into your library. A message
will be displayed for any errors or warnings encountered
during the import process.

Note:
if a PDF matches up exactly with an existing item in your
library, Paperpile will automatically attach the PDF to that
item instead of adding a duplicate entry.

Write papers in Google Docs

Paperpile's Google Docs
integration is so simple that most users need no introduction
— just create a
new document and start writing! For those who like to be
prepared, here is an overview of the main features and tips
for collaborating on academic documents with Paperpile and
Google Docs.

If you are having trouble with the Docs
plug-in, visit the troubleshooting page
for tips on how to solve the most common issues.

Inserting a citation

To insert a citation, either click the Paperpile button
in
the toolbar or use the keyboard shortcut Shift-⌘-P
(on Linux or Windows use Ctrl-Alt-P ) to open the
citation window:

Start typing to search within your library. Paperpile will
search within the title, keywords, abstract, etc. of all
papers in your library, the same as when you search from the
main Paperpile interface (example). Choose a result to add it to
the current citation:

To add another item just start searching again. Or, click
on any of the citation tags
to edit advanced options (see Advanced options for
citations below). When you have finished creating a citation,
click Add citation to add it to your document.

The citation is inserted into the Google document as a link
with placeholder text, e.g. . Note
that this is not the final formatted citation; see
below for instructions on Formatting a
bibliography.

Advanced options for citations

Clicking directly on a citation tag opens up a panel with
details and more advanced options:

The upper part of the panel shows a familiar overview of
the citation metadata with a link to open the item in
Paperpile.

Below that are three advanced citation options:

Location / page numbers: choose from a range
of location types (see a partial list) to use when citing a
specifc page, chapter, or book from within a larger
work. Example: .

Prefix / suffix: Add arbitrary text to be
included before or after the inline citation. Examples:
and .

Suppress author: this option causes citation
styles to not display the author name within inline
citations. When using a parenthetical citation style, this
allows you to include just the year in parentheses. Example:
instead of the usual .

Formatting a bibliography

After adding or editing a citation, Paperpile can reformat
your document and generate the bibliography with one
click. Simply choose Paperpile > Format citations to
proceed. (Note: you will need to give permission to
the plug-in the first time you format a document. This will
only happen once.)

To choose a different citation style, open the citation
style window with Paperpile > Citation style...:

Search for the journal or publisher whose style you would
like to use, and a preview will show in the bottom of the
window. Click Update to update the citation style
and reformat the document to see the changes.

Collaborative editing

You can edit a Paperpile-enhanced Google document with any
number of collaborators, whether or not they already use
Paperpile. Just click the Share button in the
upper-right corner of the screen and choose who to share your
document with.

If you share the document with collaborators using
Paperpile, they will be able to add new citations and reformat
the document without trouble (see our FAQ entry on how collaborative citations work). For
anyone not using Paperpile, citations and
bibliography items will link to a web-based view where you can edit or update the
data for a given item.

Important: Citing a document from your personal
Paperpile library will create a local copy specific to the
Google Document. This copy will be updated if you update the
original copy in your library. However, as soon you or someone
else edits the local copy of a Google Document any subsequent
changes you make to the original copy in your library will not
update (and thus overwrite) the local changes. Also, changes
made to the local copy by yourself or a collaborator will
never propagate back to your library.

Citation styles

Paperpile supports the popular "citation style language"
CSL with more then 8,000 citation styles available from
citationstyles.org. We
regularly update the citation styles in Paperpile so that you
always get the newest styles and updates.

To change the citation style in a Google Document go
to Paperpile > Citation
styles and search for the name of your style.

If you can't find your style you have two options: (i) find
an identical or very similar style or (ii) create your own
style. In both cases you can use the citation style editor
available
at editor.citationstyles.org.
This free web-tool allows you to find styles and to modify existing
styles to your needs.

If you have create your own CSL style, download the CSL
file to your harddisk and upload it to Paperpile
in Settings > Citation
styles. You can then select this style in your Google
document as described before.

DOIs and URLs in your citations

For most reference types Paperpile lets the citation style
control how to display DOIs and URLs.

However, for print articles Paperpile does not show DOIs or
URLs by default. More precisely, citations of types
"Journal article" and "News article" with the
field "pages" set will not include DOIs or
URLs.

To override this behavior, activate the option
"Always include DOI and URLs". This option will show
DOIs as specified by the citation style. Note, that
some citation styles don't support DOIs and this option
(despite its name) cannot change that. You may need to adapt
the behaviour of the citation style by editing the CSL file
(see above).

You can store multiple URLs in the field
"URLs". Paperpile will always use the first in
citations.

Known issues

You can only use the Google docs plugin with the same
Google account from which you signed up to Paperpile. If you
have documents owned by your non-Paperpile Google Account,
share and edit them with your Paperpile-linked account.

Sync your files with Google Drive

Here is some more information
about how synchronization of your files to Google Drive
works. Check out also the FAQs about syncing.

What you need to know about the Google Drive sync

Google Drive syncing is initially turned off. Enable
sync by clicking on the Drive icon in the top right of the
Paperpile tab.

Once enabled, all syncing takes place in the background
and no manual action is required. The Drive icon indicates
the current status of the sync process:

To check if a file is synced, open the file panel by
clicking the paperclip symbol . The drive icon indicates the sync
status of a file:

The contents in Google drive always reflects your
Paperpile library. Make any changes (e.g. delete or rename a
file) directly in Paperpile, not in Google Drive —
this is the safest way to make sure you don't see unexpected
results. However, Paperpile is smart and works hard to
automatically fix any inconsistencies encountered during
sync.

Files are arranged in folders by the first letter of the
first author's last name. All files are prefixed with
'Author year' of the reference they belong to (e.g. 'Crow
and Kimura 1970'). The main PDF for a reference is renamed
with the title, while all supplementary files maintain their
original filename (plus the 'Author year' prefix).

Troubleshooting

The drive icon says "Sync has been disabled because
of errors": Normally, if there are problems syncing your
files (e.g. Google's server is temporarily overloaded),
Paperpile will automatically try again and there is no
action required from you. However, if a problem persists and
several sync attempts fail, syncing will be disabled. Wait
some time and click the icon to re-enable sync and start a
new attempt.

One or more files did not get properly synced: If
a file is not synced, click 'Start sync now' in the drive
menu on the top right of the screen. That will force a
re-sync of all your files. It does not
re-upload any files unless necessary, so it should finish
within 1-2 minutes. If the sync is still not successful,
read on and try the next tip. Also keep in mind that files
bigger than 20Mb are currently not synced.

The sync process hangs and the Drive icons keeps
flashing forever: The Paperpile Chrome extension (which
runs invisibly whenever Chrome is running) contains the code
that actually syncs your files. Even if you reload the
Paperpile application tab, it will not completely reset the
file syncing. In the rare case that your sync is stuck for a
long time, either restart Chrome completely or reload the
extension.

Share papers with colleagues

Paperpile includes two simple yet
powerful ways to share papers: share papers via link or
email to quickly send articles to your colleagues, or
create a shared folder to create shared lists of
relevant references and PDFs with other Paperpile users.

Sharing papers via link or email

To quickly share papers, select some items from your
library and click Share > Share via Link or Email
in the toolbar. The following dialog will appear:

Your papers are ready to share — just copy the unique
sharing link and send it to your colleagues. Everyone with the
link can view the papers online (no Paperpile account is
required).

You can also enter an email address in the "Send an email"
area to have Paperpile send an email on your behalf. To
include a customized message or subject line, click "Add a
message" below the email address field (example).

When you email a paper with Paperpile your colleagues will
receive a message listing the first few items and a link to
the entire set of shared papers. If available, each paper
includes a link to the publisher's website and to your
personal copy of the PDF in Google Drive. For more details,
see the how sharing works section
below.

Creating a shared folder

Sharing with a link is quick and easy, but if you want
to add or remove papers from a shared collection
or collaborate on a shared reference list with other
Paperpile users, then a shared folder is the way to go.

Shared folders work just like regular folders in Paperpile,
except that multiple users have access to the folder and can
add and remove papers. Create shared folders for journal
clubs, reading groups, or to collaboratively collect
references for your next manuscript.

To create a shared folder, click the button next to the
area in the left pane. Alternatively, you can select a few
items your library and choose Share >
Create New Shared Folder:

Paperpile will create a new folder and pre-populate it with
your selected items (if applicable).

Click "Manage sharing" to invite new collaborators. The
following dialog will appear:

Each shared folder gets a unique link to share — this
can be shared with anyone, and provides a read-only view of
the items in your folder. To give other Paperpile users the
ability to add and remove items to and from your shared
folder, add their email addresses to the "Invite
collaborators" area.

Click Save to update the
folder's sharing settings. Email notifications will be sent,
and your collaborators will see the shared folder the next
time they open Paperpile.

Note: when you add collaborators to a shared folder,
use the same e-mail address they use for their Paperpile
account. This is usually their personal or institutional GMail
address. If you add someone using a non-Paperpile email
address, they will show up in the access list without name or
photo (example). To fix this, remove
the non-Paperpile email and add their correct address.

Working with shared folders

Anyone with access to a shared folder can do the
following:

Manage who has access: all collaborators on a
shared folder have permission to add or remove collaborators
through the "Manage Sharing" dialog. The only exception is
that nobody can remove the folder's owner. Since all
collaborators are given equal access, be sure to only invite
people who you know and trust.

Add or remove papers to or from a folder: add
papers easily by dragging one or more selected papers onto
the shared folder, or alternatively by selecting one or more
papers and choosing Share > Add to
Shared Folder from the toolbar. To remove papers from
a shared folder, make a selection and choose Remove from Folder from the
toolbar. You can remove any paper from a shared folder,
including ones not added by you.

Add or remove subfolders: click the context menu
next to a shared folder and choose Add
Subfolder to add a new folder below the selected
folder.

Copy papers to your personal library: you may
often want to take an article shared by a colleague and save
a copy in your own library for future reading, organization
or note-taking. Paperpile makes this easy by showing three
different icons for papers in a shared folder:

You added this paper to the shared
folder. Click the icon to view it in your library.

Another user has added this paper to the
shared folder, so you may add a copy to your personal
library. Click the button to copy a single paper, or
select one or more papers and choose Add to Library from the
toolbar. Paperpile will copy the paper and any available
attachments (learn how this works) to
your personal Paperpile library.

You have a copy of this paper in your
library. Click the icon to view your copy of the
paper.

Shown below is an example of three papers with three
different states: added by you, added by another user, and
added by another user with a linked copy in your library.

More info: how Paperpile sharing works

For those who would like to know more about how things work
behind the scenes, here are a few relevant technical details
behind Paperpile's sharing functionality:

Items are shared with a reference, not by
copying: when you share a paper, Paperpile creates a
reference to your personal library item, not a
copy. This means that your collaborators will always see the
latest version of the paper you added, just as it looks in
your personal library: if you edit the title, add a note, or
upload a PDF or supplementary file, all your changes will be
immediately visible to everyone. However, this also means
that if you delete an item from
your library, it will no longer be available to your
collaborators.

PDFs and attachments are shared via your Google Drive:
When someone clicks "View PDF" on a shared paper or copies
it to his or her personal library, Paperpile will generate a
read-only link to your synced Google Drive file for viewing
and downloading. This works the same as if you had chosen
"Share with a link" from within the Google Drive interface
and shared the link with your collaborators. Note:
this only works if you have enabled sync and the given
attachment has been successfully synced online.

Anonymous file downloads are restricted:
Paperpile makes it easy to collaborate on shared reading
lists and send relevant articles to your colleagues, but it
is your responsibility to ensure that you do not facilitate
illegal distribution of copyrighted works
(see
below). In practice, this means that you should be
careful who you invite to shared folders and with whom you
share a web link. To make sure no copyrighted material is
made public accidentally, shared links are excluded from
search engines and anonymous downloads of PDFs and other
files are tracked and restricted at a reasonable limit.

Sharing and copyright

It is your responsibility to respect the intellectual
property rights of the owners of any work that you organize
within Paperpile. You may only share content with other
users (including article PDFs, text, and supplementary
files) if you have the right to do so. You can share papers
if you are the copyright owner, have the copyright owner’s
permission, are permitted to do so under your publishing
agreement or your institution’s license agreement or under
license from an Open Access database or under a Creative
Commons license.

For more information, be sure to read through
our terms of service before using
Paperpile's sharing features.

Library proxy access

You can download
PDFs with restricted access while off-campus through a proxy
connection provided by your institution or library.

Select a proxy connection for your institution

Click Log in to authenticate
with the proxy server using your user name and password,
library token or other authentication method your
institution or library uses.

You can verify that the connection works
with Test connection

Add a custom proxy connection

If your institution or library is not in the list, ask your
IT department or librarian for help. If your institution
supports remote access via "EZProxy", they can provide you
with a proxy URL,
e.g. http://ezproxy.example.edu/login?url=$@. Note, the "$@" is a placeholder that tells Paperpile where to put the URL that should be accessed via the proxy server.

Add this URL to the field URL, give your connection
a name, e.g. "My university library" and
click Add Proxy Connection.
Log in and verify that the connection is working (see
above).

Using library proxy connections

If Paperpile can't access a PDF, Paperpile will re-try
downloading it through your proxy connection. You can
configure multiple connections and activate and de-activate
connections right from the main screen using the proxy
connection menu on the top right:

Always make sure you are logged in to your proxy. Follow
the "Login page" link in the proxy menu.

Paperpile will show a warning if you have configured and
activated a proxy but you are logged out.

Important notes

A few instutitions have configured their proxy access in a
way that makes it impossible to be used by Paperpile. In
particular, EZProxy servers using "Proxy by Port"
configurations are not supported. This legacy
configuration is not
not
recommended by the developers of EZproxy. We
encourage institutions to update their settings to "Proxy
by Hostname" to make their proxy access more accessible.

Your institution might use other technologies for remote
access than the "EZProxy" approach described here. Most
popular are "VPN connections" or direct proxy servers. All
these approaches are fully supported by Paperpile but need
special programs or configuration of your computer. Please
ask your library or IT department for more help.